Have you tried disconnecting the solar controller from the batteries at night? I still think it is backfeeding to the panels.
Seeing the batteries took a charge from the generator there would appear to be nothing wrong with them.
BTW you can run a much bigger charger than direct from the 12v outlet from even a 1000w generator.
A 20amp 240Volt to 12volt charger will run no problems from a generator as long as it is sine wave , although I ran mine from even an old chugga.
Regards PhilipA






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